EPACTS make-group Error

[meharji arumilli]

I have annotated the variants using annovar which gives an annotated vcf file "I1HALA.223.anno.hg19_multianno.vcf" as output.

Then i tried to create group file for nonusing epacts and met with the below message:

EPACTS-3.2.6/bin/epacts make-group --vcf I1HALA.223.anno.hg19_multianno.vcf --out nonsyn.grp --nonsyn
Succesfully create group information for 0 genes

With the help of manual i tired different ways:

$ EPACTS-3.2.6/bin/epacts make-group --vcf I1HALA.anno.vcf.hg19_multianno.vcf --out nonsense --format ANNO=[TYPE]:[GENE] --type nonsense
Succesfully create group information for 0 genes

$ EPACTS-3.2.6/bin/epacts make-group --vcf I1HALA.anno.vcf.hg19_multianno.vcf --out nonsense --format ANNO=[TYPE]:[GENE] --type nonsyn
Succesfully create group information for 0 genes

$EPACTS-3.2.6/bin/epacts make-group --vcf I1HALA.anno.vcf.hg19_multianno.vcf --out nonsense --format annovar --nonsyn
Succesfully create group information for 0 genes

$EPACTS-3.2.6/bin/epacts make-group --vcf I1HALA.anno.vcf.hg19_multianno.vcf --out nonsense --format [annovar] --nonsyn
Succesfully create group information for 0 genes

All the commands showed "Succesfully create group information for 0 genes". 

Then i tried annotating variants using EPACTS as shown below:

$ EPACTS-3.2.6/bin/epacts anno --in I1HALA.223.vcf --out I1HALA.223.epacts.vcf --ref ucsc_hg19.fa

$ EPACTS-3.2.6/bin/epacts make-group --vcf I1HALA.223.epacts.vcf --out nonsyn.grp --nonsyn
Succesfully create group information for 0 genes

It still says "Succesfully create group information for 0 genes".   Could someone help what has been going wrong?

[Iris Mathioudaki]

Hi, 

from your commands above it seems that your VCFs file are not bgzipped and tabixed. Maybe that is your problem? 

// Iris

[Hyun Min Kang]

That is correct. Same issue here.

Hyun.

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[meharji arumilli]

Hi Iris,

Here is how the vcf file is annotated using annovar:

annovar/table_annovar.pl I1HALA.223.marker_sample_QC.vcf annovar/humandb/ -buildver hg19 -protocol refGene -operation g -vcfinput -out I1HALA.223.Annovar

which outputs the file:
I1HALA.223.Annovar.hg19_multianno.vcf

Then I have compressed and indexed using bgzip and tabix before using make-group. However, i have the same issue:

$/tabix-0.2.6/bgzip -c I1HALA.223.Annovar.hg19_multianno.vcf > I1HALA.223.Annovar.hg19_multianno.vcf.gz

$/tabix-0.2.6/tabix -p vcf I1HALA.223.Annovar.hg19_multianno.vcf.gz

$ /EPACTS-3.2.6/bin/epacts make-group --vcf I1HALA.223.Annovar.hg19_multianno.vcf.gz --out I1HALA.223.nonsyn.grp --format annovar --nonsyn

Succesfully create group information for 0 genes

Could you please help.

[meharji arumilli]

Hi,

I tried to inspect a couple of points if they can offer some clue:

1. "I1HALA.223.Annovar.hg19_multianno.vcf.gz" is a multi-sample annotated vcf file generated using " table_annovar.pl"  (script from Annovar latest version which takes multisample vcf as input and outputs an annotated multisample vcf file).

Does EPACTS accept multi sample VCF file?

2. I tried annotating using "annotate_variation.pl" (traditonal script from annovar which takes in multisample vcf  and gives a non-vcf annotated output file including freq for allsamples). Few lines from output:

line1   nonsynonymous SNV       SAMD11:NM_152486:exon3:c.G166A:p.G56S,  chr1    865628  865628  G       A       0.0025  54.96   13
line2   nonsynonymous SNV       SAMD11:NM_152486:exon3:c.C232T:p.H78Y,  chr1    865694  865694  C       T       0.0075  2285.22 11
line3   nonsynonymous SNV       SAMD11:NM_152486:exon5:c.G313A:p.G105S, chr1    871159  871159  G       A       0.0075  1068.96 14

The values in column 9 are the freq values of the variant across all samples. However, the output is not in vcf format. Could this  file be fed to EPACTS?

[meharji arumilli]

Hi,

I am sharing the annovar annotated vcf file to replicate the error and suggest a fix. Please find the file at:

http://www.fileconvoy.com/dfl.php?id=ga8672222565d289c9996950576288dd7e0d767a00

Looking forward to hear back. Thank you.

On Tuesday, July 14, 2015 at 12:17:48 PM UTC+3, Ir.M wrote:

[meharji arumilli]

Dear EPACTS users,

It has been a while since my initial post regarding make-group using EPACTS. I am in terrible need of a fix as early as possible to meet a deadline. Could someone offer support to fix this issue. Thanks.

[Hyun Min Kang]

Dear Mehar,

EPACTS does not work when the chromosome names in the VCF contains 'chr' in the beginning. I suggest to run the following commands to do the annotation.

zcat I1HALA.223.Annovar.hg19_multianno.vcf.gz | sed 's/^chr//' | bgzip -c > I1HALA.223.Annovar.hg19_multianno.nochr.vcf.gz 

${EPACTS_DIR}/bin.epacts anno --in I1HALA.223.Annovar.hg19_multianno.nochr.vcf.gz --out I1HALA.223.Annovar.hg19_multianno.nochr.anno.vcf.gz

${EPACTS_DIR}/bin/epacts make-group --vcf I1HALA.223.Annovar.hg19_multianno.nochr.anno.vcf.gz --out nonsyn.grp --nonsyn

I received 'Succesfully create group information for 13755 genes' 

Thanks,

Hyun.

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[kate e]

Hi Hyun,

I am also having the same problem with the make-group command.  My files are annotated with annovar using epacts, so I know the annotation is correct.  the files are bgzipped and tabixed.

These are a couple of the commands I've been using:

/apps/well/epacts/3.2.6-R3.1-gcc472/bin/epacts make-group \

--vcf /well/hill/kate/exomes/anno/annovar_haploc/cap486_58BC/\

cap486_58BC_$chr.GQ20.biallelic.vcf.gz \

--out /well/hill/kate/exomes/epacts/cap486_58BC_$chr.LoF.grp --format annovar \

--type Start_Loss --type Stop_Gain --type Essential_Splice_Site --type Frameshift

/apps/well/epacts/3.2.6-R3.1-gcc472/bin/epacts make-group \

--vcf /well/hill/kate/exomes/anno/annovar_haploc/cap-UK10K/\

cap-UK10K_$chr.annovar.GQ20.biallelic.vcf.gz \

--out /well/hill/kate/exomes/epacts/cap-UK10K_$chr.nonsyn.grp --nonsyn

The first command works and produces grp file that looks fine.

However, the second command gives an empty file and this error:

"Succesfully create group information for 0 genes"

I've asked others if they've had the same problem and they said they had to write their own scripts to make the grp files...

Any ideas on what I might be doing wrong, or is there a bug?

Many thanks

Kate

[Arumilli, Meharji]

Hi Kate,

Make sure that your vcf file does not have "chr" notation for chromosomes chr1,chr2... Instead, they should be 1,2,3...

This is what happened in my case. Good luck.

Br
Mehar

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[kate e]

Hi Mehar,

No, definitely no "chr" in there.  I even tried using -type instead of --type since there is a discrepancy between instructions on the website and the man page.

Have written by own script to output the grp files now...

Cheers

Kate

[Hyun Min Kang]

I think EPACTS may not support latest annovar annotations. You can create your own group file pretty easily though..

Hyun.

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[Fred Boehm]

Hello, 

I read the message stating that EPACTS may not support annovar annotations, but that making your own group file may be possible. Can you recommend a method for creating a group file? What should the outputted format of the group file be? 

Thank you,

fred